Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Berta, Dénes; Buigues, Pedro J.; Badaoui, Magd; Rosta, Edina

doi:10.1016/j.sbi.2020.01.002

Cited by 26 publications

(47 citation statements)

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“…During the long history of studies of the GTP hydrolysis mechanism in GTPases [ 18 , 44 , 45 , 46 , 47 , 48 ], several proposals have been put forward concerning the role of this residue for the GTPase catalysis. There is a consensus about the importance of this residue for positioning the nucleophile water molecule for an attack on the γ-phosphate; however, a more active role of Gln61 in the Ras-GAP catalyzed GTP hydrolysis is still debated [ 30 , 31 , 32 ]. In line with the previous simulations of GTP hydrolysis by Ras-GAP [ 30 ] consistent with the glutamine-assisted mechanism, pathway-I of this reaction in Arl3-RP2 assumes that the side chain of Gln71 participates in proton transfer after cleavage of the of the O 3B –P G bond in GTP.…”

Section: Discussionmentioning

confidence: 99%

“…The subsequent steps are required to restore the enzyme. This scenario corresponds to the so-called glutamine-assisted mechanism of GTP hydrolysis by GTPases [ 27 , 28 , 29 , 30 , 31 ], according to which the catalytically important glutamine residue (Gln71, in the case of Arl3) actively participates in the reaction being a part of the proton transfer chain. We outline in Figure 1 the basic features of the reaction scheme according to [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…More precisely, we present an alternative pathway of the enzyme regeneration that better agrees with the experimental k cat values for the wild-type Arl3-RP2 complex and for the mutant in which RP2-Glu138 is replaced by glycine. It should be noted that the details of the mechanism of GTP to GDP transformation in GTPases are still under debate [ 30 , 31 , 32 ], and this particular molecular system presents an important model for simulations of GTP hydrolysis.…”

Section: Introductionmentioning

confidence: 99%

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Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

et al. 2021

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We report the results of calculations of the Gibbs energy profiles of the guanosine triphosphate (GTP) hydrolysis by the Arl3-RP2 protein complex using molecular dynamics (MD) simulations with ab initio type QM/MM potentials. The chemical reaction of GTP hydrolysis to guanosine diphosphate (GDP) and inorganic phosphate (Pi) is catalyzed by GTPases, the enzymes, which are responsible for signal transduction in live cells. A small GTPase Arl3, catalyzing the GTP → GDP reaction in complex with the activating protein RP2, constitute an essential part of the human vision cycle. To simulate the reaction mechanism, a model system is constructed by motifs of the crystal structure of the Arl3-RP2 complexed with a substrate analog. After selection of reaction coordinates, energy profiles for elementary steps along the reaction pathway GTP + H2O → GDP + Pi are computed using the umbrella sampling and umbrella integration procedures. QM/MM MD calculations are carried out, interfacing the molecular dynamics program NAMD and the quantum chemistry program TeraChem. Ab initio type QM(DFT)/MM potentials are computed with atom-centered basis sets 6-31G** and two hybrid functionals (PBE0-D3 and ωB97x-D3) of the density functional theory, describing a large QM subsystem. Results of these simulations of the reaction mechanism are compared to those obtained with QM/MM calculations on the potential energy surface using a similar description of the QM part. We find that both approaches, QM/MM and QM/MM MD, support the mechanism of GTP hydrolysis by GTPases, according to which the catalytic glutamine side chain (Gln71, in this system) actively participates in the reaction. Both approaches distinguish two parts of the reaction: the cleavage of the phosphorus-oxygen bond in GTP coupled with the formation of Pi, and the enzyme regeneration. Newly performed QM/MM MD simulations confirmed the profile predicted in the QM/MM minimum energy calculations, called here the pathway-I, and corrected its relief at the first elementary step from the enzyme–substrate complex. The QM/MM MD simulations also revealed another mechanism at the part of enzyme regeneration leading to pathway-II. Pathway-II is more consistent with the experimental kinetic data of the wild-type complex Arl3-RP2, whereas pathway-I explains the role of the mutation Glu138Gly in RP2 slowing down the hydrolysis rate.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

et al. 2021

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“… 17 The need for QM/MM methods arises in many circumstances, for example, prediction of p K a values in complex environments, accurate description of metal ions, and many more. 18 − 21 While free energy simulations (FES) with MM force fields has become routine, QM/MM calculations remain computationally demanding, which limits the applicability of QM/MM FES. 22 , 23 Furthermore, several technical tricks routinely used in MM calculations of Δ A cease to work at the QM/MM level.…”

Section: Introductionmentioning

confidence: 99%

Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations

et al. 2022

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A key step during indirect alchemical free energy simulations using quantum mechanical/molecular mechanical (QM/MM) hybrid potential energy functions is the calculation of the free energy difference Δ A low→high between the low level (e.g., pure MM) and the high level of theory (QM/MM). A reliable approach uses nonequilibrium work (NEW) switching simulations in combination with Jarzynski’s equation; however, it is computationally expensive. In this study, we investigate whether it is more efficient to use more shorter switches or fewer but longer switches. We compare results obtained with various protocols to reference free energy differences calculated with Crooks’ equation. The central finding is that fewer longer switches give better converged results. As few as 200 sufficiently long switches lead to Δ A low→high values in good agreement with the reference results. This optimized protocol reduces the computational cost by a factor of 40 compared to earlier work. We also describe two tools/ways of analyzing the raw data to detect sources of poor convergence. Specifically, we find it helpful to analyze the raw data (work values from the NEW switching simulations) in a quasi-time series-like manner. Principal component analysis helps to detect cases where one or more conformational degrees of freedom are different at the low and high level of theory.

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“…The considerable PTE activity of the A subunit, even at the end of the evolution, was beneficial for the reverse pathway from arylesterase to phosphotriesterase 31 . Quantifying the difference between the activities of the individual subunits requires state-of-the art QM/MM methods 32 because of the metal ions involved in catalysis 33 and the heterogeneity of the system 34 , 35 , which is being carried out in our laboratory using different simulation methods 32 .…”

Section: Discussionmentioning

confidence: 99%

Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer

Ambrus

Hoffka

Fuxreiter

2020

Sci Rep

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The importance of dynamic factors in enzyme evolution is gaining recognition. Here we study how the evolution of a new enzymatic activity exploits conformational tinkering and demonstrate that conversion of a dimeric phosphotriesterase to an arylesterase in Pseudomonas diminuta is accompanied by structural divergence between the two subunits. Deviations in loop conformations increase with promiscuity, leading to functionally distinct states, while they decrease during specialisation for the new function. We show that opposite loop movements in the two subunits are due to a dynamic coupling with the dimer interface, the importance of which is also corroborated by the co-evolution of the loop and interface residues. These results illuminate how protein dynamics promotes conformational heterogeneity in a dimeric enzyme, leading to alternative evolutionary pathways for the emergence of a new function.

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Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Cited by 26 publications

References 100 publications

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials

Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations

Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer

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